Below is a setup that transforms ore, crude oil, and water into speed3 and prod3 modules. I aimed at producing 2.4/minute (full output of one plant each of sp3 and pr3), but due to inefficiencies I'm stuck at about 2.2/minute.
(the whole thing takes almost 400 level 3 modules, so I guess it will take a couple hours to repay itself... but if you are aiming for a specific # of modules for a design, you could build these as modules are produced until you have enough, tear down the modules plants, and then build the design. And my 600 science per minute design requires about 12k modules....)
Raw materials are fed in on the top. It consumes two (blue) belts of copper (4.6k), one belt of iron (2.2k), some coal (450), 6.5k crude, and 9.7k water.
The ores are fed one each into a "column" of smelters and plants. The majority is comprised of green circuit production (including smelting): the first three columns until about two thirds down smelt the required copper and iron, create cables, and create the circuits. Since the smelters produce more than a full belt some ore bypasses the green circuit production feeding it from the bottom, with some copper diverted to the red circuit production on the bottom right.
Top right is the distiller column, with two refineries, cracking, and sulfur and plastic processing. These are not fully beaconed, mostly because the numbers worked out that way and it allows for piping without increasing the total footprint.
Cables and circuits are moved by bot, everything else is moved by belt (except for the plates to the sulfur plant). It seems to require just over 100 bots at full operation. Cables are moved by bot because I can't find a way to move them quick enough otherwise within the confines of the beacon rows. Since it is ultra short distance (mostly crossing the beacons) bots are pretty efficient at moving them. Circuits are moved by bot because they are low volume anyway and I couldn't find a way to include belts for moving them.
I had to put a roboport into the middle, so I decided to place it in between the green circuit plants, which allows them to output to chests next to the roboport, freeing up an extra tile so I can use six inserters to insert to copper cable and iron:
It's a bit difficult to see with all the bots flying around (we need a "hide bots" option!), but it uses 6 cable requesters, of which two are shared with iron plates. The inserters from the belt to the chest are set to insert if iron < 100. Sharing the chests this way allows the stack inserter from the belt to take its time gathering plates and allows maximal use of the inserters into the green plant. (a green plant consumes 5.5 * 2 * (2+10) = 132 items/sec, so theoretically 5 inserters should be able to move this, but I couldn't get them to full production without the sixth inserter).
The same "chest sharing" technique is used for the red circuits, allowing enough space to pass through the copper plates and pipe the sulfur gas down to the blue plants.
The modules are produced at the bottom. The level 1 and 2 modules needed 3 beacons each to get enough production with only 4 cq 2 plants, so by placing them at the end of the column they get the right boost. The level 3 modules don't need to be boosted. Alternatively you can add a full 4-2-1 for both speed and production and switch according to need to make it more responsive.
production
helmod
You can probably improve this design as it was mostly built by trial and error. Of course it pisses me off that it doesn't quite get full production... I think the bottleneck is iron to the green circuit plants, so maybe using bots to move these as well could help. 
blueprint